Lily Owens begins her adventure with bees in the summer of 1964. She is fourteen years old, and she lives in Sylvan, South Carolina, with her abusive father, T. Ray, and her housekeeper, Rosaleen. Lily’s mother died when she was four years old. Her only memory of her mother is from the day she died; Lily recalls that she may have picked up a gun and accidentally killed her mother.
The day the Civil Rights Act is passed, Rosaleen decides that she is going to register to vote. To avoid the monotony on the Owens’ peach farm, Lily accompanies Rosaleen. On the way to register, Rosaleen gets harassed by local racist white men. Rosaleen’s response is to pour snuff spit all over their shoes, getting herself beaten severely by her accusers and arrested.
T. Ray picks up Lily at the police station, and the two of them get into a fight. T. Ray finally tells Lily that her mother left her, angering Lily enough that she runs away. Lily goes to pick up Rosaleen, and she ultimately has to sneak Rosaleen out of the hospital. The two of them hitchhike to Tiburon, South Carolina. Lily picks this city because she once found her mother’s picture of a black Mary with the town etched into the back.
Lily and Rosaleen successfully get a ride to Tiburon and spend a night in the woods. The next day, Lily enters a general store and finds that her mother’s black Mary picture matches the labels on jars of Black Madonna Honey. Lily asks the store owner, Mr. Grady, to direct her to where the honey is made. He sends Lily to the Boatwrights’ pink house.
Upon reaching the Boatwrights’ house, Lily lies about her intentions. She says that she is an orphan with nowhere to stay and is on her way to visit her aunt. She meets the family of three black sisters. August Boatwright invites them to stay as long as they need. May Boatwright carries the weight of the world in her heart, and June Boatwright is not pleased with Lily staying in their house. The women have a group of friends called the Daughters of Mary, and all of them together worship Our Lady of Chains, a black Mary who was able to break the chains that bound her.
In return for her room and board, Lily is required to assist August with the beekeeping. Lily learns how the bee world reflects the human world, and she learns to send love to the bees. She begins to love her life in Tiburon, but she feels awful about keeping her secret from August.
After a week at the Boatwrights’, Lily meets Zach, a black boy who works in the bee yard. She instantly is taken by how handsome he is, and she is surprised by her own ability to be attracted to a black boy. The two of them get to know each other and shortly fall in love.
It is about this point that Lily finds May participating in an old habit of Deborah’s, making trails of crumbs to lead bugs out of the house. Lily decides to ask May if May ever knew Lily’s mother, and May confirms that Deborah lived in the honey house for a while. Lily becomes obsessed with the idea that her mother was in the same place that she is.
On one outing to put honey jars in an office, Zach runs into his friend Jackson and two other boys. They are confronted by a group of white men who are prepared to protest against a white movie star attending a movie with a black woman, as the rumor goes. Jackson throws a bottle at one of the white men, and the four black boys, Zach included, are all put in jail.
The Boatwrights and their friend Attorney Clayton Forrest all do their best to get Zach out of jail. However, they must wait. They visit him, but they have to be patient until Judge Monroe returns to his office. In the meantime, June, August, and Rosaleen resolve not to tell May about Zach’s incarceration.
One night, while the family is watching television, May answers the phone and speaks with Zach’s mother. This is how May learns that Zach had been jailed. May feels upset that no one told her about the incident before, and she is upset for Zach himself. She decides to partake in her usual ritual to relieve her pain: going out to her “wailing wall.” This time, May does not come back. The other women find her dead in the river, having killed herself.
Riddled with grief, the family sits with May’s body in the living room in order to prepare for the burial. The Daughters of Mary sit and make jokes about white funerals, and Lily finally feels that she has been accepted as one of them. On the day of May’s funeral, Lily recalls the hum of the bees surrounding them.
A few days after the funeral, the Boatwright house celebrates Mary’s Day, a two-day commemoration of the Feast of the Assumption. The women bake, decorate, and reenact the story of Our Lady in Chains. After the first night of the Mary Day celebration, Lily decides to come clean with August. She tells August all about her past and how she got to Tiburon. In turn, August tells Lily about her mother’s upbringing and tells Lily that Deborah left Lily in Sylvan to come to the Boatwright house. Lily is left with mixed emotions of both anger and pity for her mother.
That night, Lily trashes the honey house out of anger. She breaks jars of honey and throws buckets. She eventually tires herself out and falls asleep. Rosaleen wakes her, and the two of them clean up the honey house. For the second day of Mary’s Day, Lily is bitter. It is not until the Daughters participate in the ritual of massaging Our Lady with honey that Lily cheers up. She becomes content working with the women to preserve the statue.
That evening, August comes to the honey house with a box of Lily’s mother’s belongings. Lily receives a mirror, a brush, and a whale pin that belonged to her mother. Most importantly, August hands Lily a photo of Deborah and Lily smiling at each other. Lily realizes that her mother did love her and cherish her as a mother should. At this point, Lily falls into grief, missing her mother more than ever.
Still in a bit of a funk, Lily does not accompany Rosaleen to register to vote in Tiburon. Instead, she spends the day writing in her notebook. A knock at the door reveals that T. Ray has come to take her back to Sylvan. Lily negotiates, and T. Ray becomes enraged and confused by Deborah’s earlier interaction with the Boatwrights. Lily realizes that T. Ray must have loved Deborah deeply, and he must have fallen into depression when she died. It becomes clear that T. Ray does not need Lily around him after all, for she reminds him of Deborah, so he allows her to remain in the care of the Boatwrights.
In the fall, June gets married and Lily starts school. Zach has decided to go to the white school with Lily. Clayton Forrest gives his assurance that Lily and Rosaleen are not getting charged with any crimes back in Sylvan. Lily feels blessed that she is surrounded by the love of her many Tiburon mothers.